this is a known issue with Eagle 4.1 and composite managers, see
http://www.cadsoft.de/faq.htm#17040701

a solution is to set the XLIB_SKIP_ARGB_VISUALS environment variable to
1 before starting eagle:

XLIB_SKIP_ARGB_VISUALS=1 /usr/lib/eagle/bin/eagle

this worked for me

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eagle layout editor missbehave when compositor manager is turned on
https://bugs.launchpad.net/bugs/110479
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